.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.15.
.TH FILTERSEQ.PY "1" "May 2020" "FilterSeq.py 0.6.0" "User Commands"
.SH NAME
FilterSeq.py \- Filters sequences in FASTA/FASTQ files
.SH DESCRIPTION
usage: FilterSeq.py [\-\-version] [\-h]  ...
.PP
Filters sequences in FASTA/FASTQ files
.SS "help:"
.TP
\fB\-\-version\fR
show program's version number and exit
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.SS "subcommands:"
.IP
Filtering operation
.TP
length
Filters reads by length.
.TP
missing
Filters reads by N or gap character count.
.TP
repeats
Filters reads by consecutive nucleotide repeats.
.TP
quality
Filters reads by quality score.
.TP
maskqual
Masks low quality positions.
.TP
trimqual
Trims sequences by quality score decay.
.SS "output files:"
.IP
<command>\-pass
.IP
reads passing filtering operation and modified accordingly, where
<command> is the name of the filtering operation that was run.
.IP
<command>\-fail
.IP
raw reads failing filtering criteria, where <command> is the name of
the filtering operation.
.SS "output annotation fields:"
.IP
None
.SH AUTHOR
 This manpage was written by Andreas Tille for the Debian distribution and
 can be used for any other usage of the program.